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Coexpression cluster:C3326: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!8.87e-26!89;UBERON:0001017!1.14e-25!81;UBERON:0001049!5.50e-25!56;UBERON:0005068!5.50e-25!56;UBERON:0006241!5.50e-25!56;UBERON:0007135!5.50e-25!56;UBERON:0000073!2.55e-23!53;UBERON:0002616!2.55e-23!53;UBERON:0000955!3.99e-22!68;UBERON:0006238!3.99e-22!68;UBERON:0002346!1.17e-21!86;UBERON:0003075!4.50e-20!82;UBERON:0007284!4.50e-20!82;UBERON:0002780!2.40e-19!41;UBERON:0001890!2.40e-19!41;UBERON:0003080!2.40e-19!41;UBERON:0006240!2.40e-19!41;UBERON:0004121!3.95e-18!171;UBERON:0000924!3.95e-18!171;UBERON:0006601!3.95e-18!171;UBERON:0003528!4.34e-17!34;UBERON:0002020!4.34e-17!34;UBERON:0011216!6.47e-17!223;UBERON:0010371!4.67e-16!104;UBERON:0002791!6.91e-16!32;UBERON:0001893!7.30e-16!34;UBERON:0001869!1.95e-15!32;UBERON:0003056!2.64e-14!61;UBERON:0010314!2.69e-14!132;UBERON:0007023!3.71e-13!114;UBERON:0000477!5.88e-13!373;UBERON:0000956!1.24e-12!25;UBERON:0000203!1.24e-12!25;UBERON:0002619!2.06e-12!22;UBERON:0001950!3.74e-11!20;UBERON:0000481!7.61e-10!342;UBERON:0000064!9.14e-08!218;UBERON:0000468!1.67e-07!656;UBERON:0004111!1.77e-07!240;UBERON:0000483!2.12e-07!306;UBERON:0000119!6.00e-07!309;UBERON:0003076!7.20e-07!15;UBERON:0003057!7.20e-07!15
|ontology_enrichment_uberon=UBERON:0001016!8.87e-26!89;UBERON:0001017!1.14e-25!81;UBERON:0001049!5.50e-25!56;UBERON:0005068!5.50e-25!56;UBERON:0006241!5.50e-25!56;UBERON:0007135!5.50e-25!56;UBERON:0000073!2.55e-23!53;UBERON:0002616!2.55e-23!53;UBERON:0000955!3.99e-22!68;UBERON:0006238!3.99e-22!68;UBERON:0002346!1.17e-21!86;UBERON:0003075!4.50e-20!82;UBERON:0007284!4.50e-20!82;UBERON:0002780!2.40e-19!41;UBERON:0001890!2.40e-19!41;UBERON:0003080!2.40e-19!41;UBERON:0006240!2.40e-19!41;UBERON:0004121!3.95e-18!171;UBERON:0000924!3.95e-18!171;UBERON:0006601!3.95e-18!171;UBERON:0003528!4.34e-17!34;UBERON:0002020!4.34e-17!34;UBERON:0011216!6.47e-17!223;UBERON:0010371!4.67e-16!104;UBERON:0002791!6.91e-16!32;UBERON:0001893!7.30e-16!34;UBERON:0001869!1.95e-15!32;UBERON:0003056!2.64e-14!61;UBERON:0010314!2.69e-14!132;UBERON:0007023!3.71e-13!114;UBERON:0000477!5.88e-13!373;UBERON:0000956!1.24e-12!25;UBERON:0000203!1.24e-12!25;UBERON:0002619!2.06e-12!22;UBERON:0001950!3.74e-11!20;UBERON:0000481!7.61e-10!342;UBERON:0000064!9.14e-08!218;UBERON:0000468!1.67e-07!656;UBERON:0004111!1.77e-07!240;UBERON:0000483!2.12e-07!306;UBERON:0000119!6.00e-07!309;UBERON:0003076!7.20e-07!15;UBERON:0003057!7.20e-07!15
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}}
}}

Revision as of 16:04, 26 November 2012


Full id: C3326_parietal_pineal_neuroectodermal_Cardiac_occipital_temporal_Neurons



Phase1 CAGE Peaks

Hg19::chr12:7045535..7045576,+p3@ATN1
Hg19::chr12:7045821..7045845,+p2@L10377
Hg19::chr12:7051290..7051449,+p@chr12:7051290..7051449
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
nervous system8.87e-2689
central nervous system1.14e-2581
neural tube5.50e-2556
neural rod5.50e-2556
future spinal cord5.50e-2556
neural keel5.50e-2556
regional part of nervous system2.55e-2353
regional part of brain2.55e-2353
brain3.99e-2268
future brain3.99e-2268
neurectoderm1.17e-2186
neural plate4.50e-2082
presumptive neural plate4.50e-2082
regional part of forebrain2.40e-1941
forebrain2.40e-1941
anterior neural tube2.40e-1941
future forebrain2.40e-1941
ectoderm-derived structure3.95e-18171
ectoderm3.95e-18171
presumptive ectoderm3.95e-18171
brain grey matter4.34e-1734
gray matter4.34e-1734
organ system subdivision6.47e-17223
ecto-epithelium4.67e-16104
regional part of telencephalon6.91e-1632
telencephalon7.30e-1634
cerebral hemisphere1.95e-1532
pre-chordal neural plate2.64e-1461
structure with developmental contribution from neural crest2.69e-14132
adult organism3.71e-13114
anatomical cluster5.88e-13373
cerebral cortex1.24e-1225
pallium1.24e-1225
regional part of cerebral cortex2.06e-1222
neocortex3.74e-1120
multi-tissue structure7.61e-10342
organ part9.14e-08218
multi-cellular organism1.67e-07656
anatomical conduit1.77e-07240
epithelium2.12e-07306
cell layer6.00e-07309
posterior neural tube7.20e-0715
chordal neural plate7.20e-0715
Disease
Ontology termp-valuen
cell type cancer1.09e-08143


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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